Origin IGS: ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttaaatcctcctaatatggttatattttaaatataacgcaacggtcctttgtgggaaaggttaaattatactttacaattatattattttttttagataatgtcaataaataaaatttatgttatctaaatttttcttattgacaaaaatataaaaaagtgataatatttccatcataaaaactgaataaataatcggatgaagatatgaggagagatttcattttaatgaaacaccgaagaagtaaatctttcaggtaaaaaggactcatattggacgaacctctggagagcttatctaagagataacaccgaaggagcaaagctaattttagcctaaactctcaggtaaaaggacggagtaattgtgcaatttatatttttaatatattttaaaatatattttttat Mask Tandem Repeat Region ================================================ ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Find is-nt database================================================ Query_seq: FN0328:FN0329|FN0328:FN0329:Na(+)-linked D-alanine glycine permease:50S ribosomal protein L13:<-->:963862..964272 411 ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0328:FN0329|FN0328:FN0329:Na(+)-linked D-alanine glycine permease:50S ribosomal protein L13:<-->:963862..964272 411 ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0328:FN0329|FN0328:FN0329:Na(+)-linked D-alanine glycine permease:50S ribosomal protein L13:<-->:963862..964272 411 ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 88 End: 270 ....................................................................................... M L L R C Y L L D K L S R G S S N M S P F Y L K D L L L R C F I K M K S L L I S S S D Y L F S F Y D G N I I T F L Y F C ............................................................................................................................................. Protein_Len: 30 Strand: + Start: 215 End: 304 ...................................................................................................................................................................................................................... M I Y S V F M M E I L S L F Y I F V N K K N L D N I N F I Y ........................................................................................................... ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 90 Start: 303 End: 332 ..............................................................................................................................................................................................................................................................................................................ATTGACATTATCTAAAAAAAATAATATAAT............................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 242 End: 271 .................................................................................................................................................................................................................................................ATTGACAAAAATATAAAAAAGTGATAATAT............................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 351 End: 380 ..............................................................................................................................................................................................................................................................................................................................................................CTTTCCCACAAAGGACCGTTGCGTTATATT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -8.3 Tail_Score: -3.48395 Start: 265 End: 309 Full_Region: ACTTTTTTATATTTT TGTCAATAAGAAAAATTTA GATAACA TAAATTTTATTTATTGACA TTATCTAAAAAAAAT ........................................................................................................................................................................................................................................................................TGTCAATAAGAAAAATTTAGATAACATAAATTTTATTTATTGACA...................................................................................................... TransTerm Strand: - Conf: 68 HP_score: -2.0 Tail_Score: -5.29445 Start: 280 End: 318 Full_Region: aattatattattttt tttagataatgtcaat aaataaa atttatgttatctaaa tttttcttattgaca .......................................................................................................................................................................................................................................................................................tttagataatgtcaataaataaaatttatgttatctaaa............................................................................................. Find igs database================================================ Query_seq: FN0328:FN0329|FN0328:FN0329:Na(+)-linked D-alanine glycine permease:50S ribosomal protein L13:<-->:963862..964272 411 ataaaaaatatattttaaaatatattaaaaatataaattgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccgattatttattcagtttttatgatggaaatattatcacttttttatatttttgtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Intra-Species Hit: Count: 1 Min: 39 Max: 411 Len: 373 Subject: NC_003454_FN0328_FN0329|Na(+)-linked D-alanine glycine permease:50S ribosomal protein L13|NEGATIVE:POSITIVE|[963862,964272]|411 HSP 1 e-value: 5.0E-95 bit: 349.0 Len: 176 Query Start:39 Query End:214 Subject Strand: POSITIVE Subject Start: 39 Subject End: 214 ......................................tgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccg..................................................................................................................................................................................................... ......................................tgcacaattactccgtccttttacctgagagtttaggctaaaattagctttgctccttcggtgttatctcttagataagctctccagaggttcgtccaatatgagtcctttttacctgaaagatttacttcttcggtgtttcattaaaatgaaatctctcctcatatcttcatccg..................................................................................................................................................................................................... HSP 2 e-value: 8.0E-63 bit: 242.0 Len: 146 Query Start:266 Query End:411 Subject Strand: POSITIVE Subject Start: 266 Subject End: 411 .........................................................................................................................................................................................................................................................................gtcaataagaaaaatttagataacataaattttatttattgacattatctnnnnnnnntaatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa .........................................................................................................................................................................................................................................................................gtcaataagaaaaatttagataacataaattttatttattgacattatctaaaaaaaataatataattgtaaagtataatttaacctttcccacaaaggaccgttgcgttatatttaaaatataaccatattaggaggatttaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCACAAUUACUCCGUCCUUUUACCUGAGAGUUUAGGCUAAAAUUAGCUUUGCUCCUUCGGUGUUAUCUCUUAGAUAAGCUCUCCAGAGGUUCGUCCAAUAUGAGUCCUUUUUACCUGAAAGAUUUACUUCUUCGGUGUUUCAUUAAAAUGAAAUCUCUCCUCAUAUCUUCAUCCGAUUAUUUAUUCAGUUUUUAUGAUGGAAAUAUUAUCACUUUUUUAUAUUUUUGUCAAUAAGAAAAAUUUAGAUAACAUAAAUUUUAUUUAUUGACAUUAUCUAAAAAAAAUAAUAUAAUUGUAAAGUAUAAUUUAACCUUUCCCACAAAGGACCGUUGCGUUAUAUUUAAAAUAUAACCAUAUUAGGAGGAUUUAAAA ..............(((((((((.((((((((..((((((....)))))).))))..((((((..((((((.(((.....)))..)))))).......(((((((..........(((((.((......))))))).(((((((....))))))).....)))))))...)).))))........))))........((((..(((((((...(((((((.((...((((((((((.((((((((.......)))))))).))))))))))..)).))))))).))))))).......(((((((((.((((...(((......)))..)))).))))))))).........))))..)))))))))...... (-77.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAAUCCUCCUAAUAUGGUUAUAUUUUAAAUAUAACGCAACGGUCCUUUGUGGGAAAGGUUAAAUUAUACUUUACAAUUAUAUUAUUUUUUUUAGAUAAUGUCAAUAAAUAAAAUUUAUGUUAUCUAAAUUUUUCUUAUUGACAAAAAUAUAAAAAAGUGAUAAUAUUUCCAUCAUAAAAACUGAAUAAAUAAUCGGAUGAAGAUAUGAGGAGAGAUUUCAUUUUAAUGAAACACCGAAGAAGUAAAUCUUUCAGGUAAAAAGGACUCAUAUUGGACGAACCUCUGGAGAGCUUAUCUAAGAGAUAACACCGAAGGAGCAAAGCUAAUUUUAGCCUAAACUCUCAGGUAAAAGGACGGAGUAAUUGUGCA .......((.(((.(((((((((((((.....))))))).....((((((((....((((((((......((((((.......((((((((((((.......(((((((((..((((((((.......))))))))..))))))))).......))))))))))))...(((((.(((((....((((........)))).......))))))))))..((((((....)))))).......))))))))))))))......))))))))))))))))).))..(((((......((((((.((((.......(....)......((((....)))).....)))).)))))).....))))).......... (-81.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 957 100 51 229 180 NC_003454:FN0328|5end_Na(+)-linked_D-alanine_glycine_permease_963771..964001_NEGATIVE 300 68 24 92 42 NC_003454:FN1560|5end_hypothetical_protein_82982..83212_NEGATIVE 290 59 15 106 64 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 269 96 51 169 122 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 264 59 12 231 185 NC_003454:FN0197|5end_Methyltransferase_822664..822894_POSITIVE 263 59 24 142 102 NC_003454:FN0295|5end_Transketolase_927986..928216_POSITIVE 254 89 44 131 66 NC_003454:FN1329|5end_Methyltransferase_1983890..1984120_NEGATIVE 245 120 81 225 189 NC_003454:FN1600|5end_tRNA_pseudouridine_synthase_A_109812..110042_NEGATIVE 244 57 12 59 17 NC_003454:FN0438|5end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1080822..1081052_NEGATIVE 241 192 153 113 78 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 235 59 13 179 139 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 234 139 91 55 5 NC_003454:FN0784|5end_Electron_transfer_flavoprotein_beta-subunit_1440332..1440562_POSITIVE 234 58 11 105 58 NC_003454:FN1537|5end_Arsenical_pump-driving_ATPase_51112..51342_NEGATIVE 233 143 102 65 36 NC_003454:FN1298|5end_Adenylate_kinase_1955626..1955856_NEGATIVE 232 170 127 231 192 NC_003454:FN1457|5end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2138976..2139206_NEGATIVE 231 209 166 65 11 NC_003454:FN1124|5end_Outer_membrane_porin_F_1769005..1769235_NEGATIVE 230 70 26 185 145 NC_003454:FN0769|5end_Hemin_transport_system_permease_protein_hmuU_1425704..1425934_POSITIVE 230 58 11 105 43 NC_003454:FN0439|5end_hypothetical_protein_1081610..1081840_NEGATIVE 230 54 11 147 98 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 228 177 139 168 128 NC_003454:FN0973|5end_Histidinol-phosphate_aminotransferase_1626699..1626929_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 59 15 105 63 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE 269 96 51 150 103 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 263 59 24 117 77 NC_003454:FN0294|3end_Transketolase_subunit_A_928041..928191_POSITIVE 254 89 44 118 53 NC_003454:FN1330|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1983903..1984053_NEGATIVE 252 88 44 95 37 NC_003454:FN0447|3end_NIFS_protein_1090574..1090724_POSITIVE 245 98 53 151 111 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 244 57 12 44 2 NC_003454:FN0439|3end_hypothetical_protein_1080837..1080987_NEGATIVE 241 192 153 101 66 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 240 180 137 93 46 NC_003454:FN1454|3end_D-alanine--D-alanine_ligase_2134796..2134946_NEGATIVE 236 95 53 128 96 NC_003454:FN0535|3end_hypothetical_protein_1190009..1190159_POSITIVE 236 68 29 42 1 NC_003454:FN1561|3end_Hypothetical_cytosolic_protein_83032..83182_NEGATIVE 234 58 11 108 61 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 230 54 11 145 96 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 228 177 139 151 111 NC_003454:FN0974|3end_Lactoylglutathione_lyase_1626716..1626866_NEGATIVE 225 176 155 115 89 NC_003454:FN1875|3end_Peptidyl-prolyl_cis-trans_isomerase_363906..364056_NEGATIVE 224 66 24 60 21 NC_003454:FN0527|3end_Alanyl-tRNA_synthetase_1182977..1183127_NEGATIVE 223 87 46 106 66 NC_003454:FN0996|3end_Hypothetical_membrane-spanning_protein_1650673..1650823_NEGATIVE 223 239 198 74 31 NC_003454:FN0775|3end_putative_aminopeptidase_2_1431937..1432087_POSITIVE 220 61 25 52 17 NC_003454:FN0008|3end_quinolinate_synthetase_648986..649136_POSITIVE 218 134 91 102 59 NC_003454:FN0548|3end_Regulatory_protein_recX_1201409..1201559_POSITIVE